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Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 5-chlorouracil, Form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A7N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 293 Potassium bromide, Polyethylene glycol monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 1.96 37.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.37 α = 90 b = 43.78 β = 98.46 c = 67.23 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2013-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.88 36.91 99.9 0.093 9.6 3 16412
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.98 99.6 0.39 2.8 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3A7N 1.88 36.91 15579 830 99.8 0.14362 0.14158 0.1559 0.18187 0.1885 RANDOM 16.659
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.89 -0.68 -0.22 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.634 r_dihedral_angle_4_deg 19.846 r_dihedral_angle_3_deg 13.663 r_dihedral_angle_1_deg 6.362 r_long_range_B_refined 5.787 r_long_range_B_other 5.519 r_scangle_other 3.568 r_scbond_it 2.314 r_scbond_other 2.313 r_mcangle_it 2.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.634 r_dihedral_angle_4_deg 19.846 r_dihedral_angle_3_deg 13.663 r_dihedral_angle_1_deg 6.362 r_long_range_B_refined 5.787 r_long_range_B_other 5.519 r_scangle_other 3.568 r_scbond_it 2.314 r_scbond_other 2.313 r_mcangle_it 2.203 r_mcangle_other 2.202 r_angle_refined_deg 1.985 r_mcbond_it 1.423 r_mcbond_other 1.423 r_angle_other_deg 0.972 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1704 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing